Clean up Doxygen docs and comments in Reactor classes

include/cantera/zeroD/ConstPressureReactor.h

@@ -1,6 +1,4 @@
-/**
+//! @file ConstPressureReactor.h
- *  @file ConstPressureReactor.h
- */
 
 // Copyright 2001  California Institute of Technology
 

include/cantera/zeroD/FlowDevice.h

@@ -1,6 +1,4 @@
-/**
+//! @file FlowDevice.h
- *  @file FlowDevice.h
- */
 
 // Copyright 2001  California Institute of Technology
 
@@ -39,9 +37,7 @@ public:
         return m_type;
     }
 
-    /*!
+    //! Mass flow rate (kg/s).
-     * Mass flow rate (kg/s).
-     */
     doublereal massFlowRate(double time = -999.0) {
         if (time != -999.0) {
             updateMassFlowRate(time);
@@ -53,17 +49,15 @@ public:
     //! subclassess to update m_mdot.
     virtual void updateMassFlowRate(doublereal time) {}
 
-    /*!
+    //! Mass flow rate (kg/s) of outlet species k. Returns zero if this species
-     * Mass flow rate (kg/s) of outlet species k. Returns zero if this species
+    //! is not present in the upstream mixture.
-     * is not present in the upstream mixture.
-     */
     doublereal outletSpeciesMassFlowRate(size_t k);
 
     //! specific enthalpy
     doublereal enthalpy_mass();
 
-    /**
+    //! Install a flow device between two reactors.
-     * Install a flow device between two reactors.
+    /*!
      * @param in Upstream reactor.
      * @param out Downstream reactor.
      */

include/cantera/zeroD/FlowReactor.h

@@ -1,6 +1,4 @@
-/**
+//! @file FlowReactor.h
- *  @file FlowReactor.h
- */
 
 // Copyright 2001  California Institute of Technology
 
@@ -12,9 +10,7 @@
 namespace Cantera
 {
 
-/**
+//! Adiabatic flow in a constant-area duct.
- * Adiabatic flow in a constant-area duct.
- */
 class FlowReactor : public Reactor
 {
 public:

include/cantera/zeroD/IdealGasConstPressureReactor.h

@@ -1,6 +1,4 @@
-/**
+//! @file ConstPressureReactor.h
- *  @file ConstPressureReactor.h
- */
 
 // Copyright 2001  California Institute of Technology
 
@@ -14,11 +12,10 @@ namespace Cantera
 
 /**
  * Class ConstPressureReactor is a class for constant-pressure reactors. The
- * reactor may have an arbitrary number of inlets and outlets, each of which
+ * reactor may have an arbitrary number of inlets and outlets, each of which may
- * may be connected to a "flow device" such as a mass flow controller, a
+ * be connected to a "flow device" such as a mass flow controller, a pressure
- * pressure regulator, etc. Additional reactors may be connected to the other
+ * regulator, etc. Additional reactors may be connected to the other end of the
- * end of the flow device, allowing construction of arbitrary reactor
+ * flow device, allowing construction of arbitrary reactor networks.
- * networks.
  */
 class IdealGasConstPressureReactor : public ConstPressureReactor
 {

include/cantera/zeroD/IdealGasReactor.h

@@ -1,6 +1,4 @@
-/**
+//! @file IdealGasReactor.h
- *  @file IdealGasReactor.h
- */
 
 // Copyright 2001  California Institute of Technology
 

include/cantera/zeroD/Reactor.h

@@ -1,6 +1,4 @@
-/**
+//! @file Reactor.h
- *  @file Reactor.h
- */
 
 // Copyright 2001  California Institute of Technology
 
@@ -45,9 +43,8 @@ public:
     }
 
     /**
-     * Insert something into the reactor. The 'something' must
+     * Insert something into the reactor. The 'something' must belong to a class
-     * belong to a class that is a subclass of both ThermoPhase
+     * that is a subclass of both ThermoPhase and Kinetics.
-     * and Kinetics.
      */
     template<class G>
     void insert(G& contents) {
@@ -168,13 +165,13 @@ protected:
     //! specific reactor implementations.
     virtual size_t speciesIndex(const std::string& nm) const;
 
-    //! Evaluate terms related to Walls
+    //! Evaluate terms related to Walls. Calculates #m_vdot and #m_Q based on
-    //! Calculates #m_vdot and #m_Q based on wall movement and heat transfer
+    //! wall movement and heat transfer.
     //! @param t     the current time
     virtual void evalWalls(double t);
 
-    //! Evaluate terms related to surface reactions
+    //! Evaluate terms related to surface reactions. Calculates #m_sdot and rate
-    //! Calculates #m_sdot and rate of change in surface species coverages
+    //! of change in surface species coverages.
     //! @param t          the current time
     //! @param[out] ydot  array of d(coverage)/dt for surface species
     //! @returns          Net mass flux from surfaces

include/cantera/zeroD/ReactorBase.h

@@ -1,6 +1,5 @@
-/**
+//! @file ReactorBase.h
- *  @file ReactorBase.h
+
- */
 // Copyright 2001  California Institute of Technology
 
 #ifndef CT_REACTORBASE_H
@@ -51,19 +50,14 @@ public:
     //! @name Methods to set up a simulation.
     //@{
 
-    /**
+    //! Set the initial reactor volume. By default, the volume is 1.0 m^3.
-     * Set the initial reactor volume. By default, the volume is
-     * 1.0 m^3.
-     */
     void setInitialVolume(doublereal vol) {
         m_vol = vol;
     }
 
-    /**
+    //! Specify the mixture contained in the reactor. Note that a pointer to
-     * Specify the mixture contained in the reactor. Note that
+    //! this substance is stored, and as the integration proceeds, the state of
-     * a pointer to this substance is stored, and as the integration
+    //! the substance is modified.
-     * proceeds, the state of the substance is modified.
-     */
     virtual void setThermoMgr(thermo_t& thermo);
 
     //! Connect an inlet FlowDevice to this reactor
@@ -80,8 +74,7 @@ public:
     //! reactor.
     FlowDevice& outlet(size_t n = 0);
 
-    //! Return the number of inlet FlowDevice objects connected to this
+    //! Return the number of inlet FlowDevice objects connected to this reactor.
-    //! reactor.
     size_t nInlets() {
         return m_inlet.size();
     }

include/cantera/zeroD/ReactorFactory.h

@@ -1,6 +1,5 @@
-/**
+//! @file ReactorFactory.h
- *  @file ReactorFactory.h
+
- */
 // Copyright 2001  California Institute of Technology
 
 #ifndef REACTOR_FACTORY_H

include/cantera/zeroD/ReactorNet.h

@@ -1,6 +1,5 @@
-/**
+//! @file ReactorNet.h
- *  @file ReactorNet.h
+
- */
 // Copyright 2004  California Institute of Technology
 
 #ifndef CT_REACTORNET_H
@@ -29,11 +28,8 @@ public:
     //! @name Methods to set up a simulation.
     //@{
 
-    /**
+    //! Set initial time. Default = 0.0 s. Restarts integration from this time
-     * Set initial time. Default = 0.0 s. Restarts integration
+    //! using the current mixture state as the initial condition.
-     * from this time using the current mixture state as the
-     * initial condition.
-     */
     void setInitialTime(doublereal time) {
         m_time = time;
         m_integrator_init = false;
@@ -232,17 +228,15 @@ public:
     }
 
 protected:
-    /**
+    //! Initialize the reactor network. Called automatically the first time
-     * Initialize the reactor network. Called automatically the first time
+    //! advance or step is called.
-     * advance or step is called.
-     */
     void initialize();
 
     std::vector<Reactor*> m_reactors;
     Integrator* m_integ;
     doublereal m_time;
     bool m_init;
-    bool m_integrator_init; //! True if integrator initialization is current
+    bool m_integrator_init; //!< True if integrator initialization is current
     size_t m_nv;
 
     //! m_start[n] is the starting point in the state vector for reactor n
@@ -264,12 +258,12 @@ protected:
     std::vector<std::string> m_paramNames;
 
     //! Structure used to determine the order of sensitivity parameters
-    //! m_sensOrder[Reactor or Wall, leftright][reaction number] = parameter index
+    //! m_sensOrder[Reactor or Wall, leftright][reaction number] = parameter
+    //! index
     std::map<std::pair<void*, int>, std::map<size_t, size_t> > m_sensOrder;
 
-    //! Mapping from the order in which sensitivity parameters were added to
+    //! Mapping from the order in which sensitivity parameters were added to the
-    //! the ReactorNet to the order in which they occur in the integrator
+    //! ReactorNet to the order in which they occur in the integrator output.
-    //! output.
     std::vector<size_t> m_sensIndex;
 
     vector_fp m_ydot;

include/cantera/zeroD/Reservoir.h

@@ -1,6 +1,5 @@
-/**
+//! @file Reservoir.h
- * @file Reservoir.h
+
- */
 // Copyright 2001  California Institute of Technology
 
 #ifndef CT_RESERVOIR_H

include/cantera/zeroD/Wall.h

@@ -1,7 +1,5 @@
-/**
+//! @file Wall.h Header file for class Wall.
- *  @file Wall.h
+
- *  Header file for class Wall.
- */
 // Copyright 2001-2004  California Institute of Technology
 
 #ifndef CT_WALL_H
@@ -32,8 +30,11 @@ public:
     virtual ~Wall() {}
 
     //! Rate of volume change (m^3/s) for the adjacent reactors.
-    /*! The volume rate of change is given by
+    /*!
-     * \f[ \dot V = K A (P_{left} - P_{right}) + F(t) \f]
+     * The volume rate of change is given by
+     * \f[
+     *     \dot V = K A (P_{left} - P_{right}) + F(t)
+     * \f]
      * where *K* is the specified expansion rate coefficient, *A* is the wall
      * area, and *F(t)* is a specified function of time. Positive values for
      * `vdot` correspond to increases in the volume of reactor on left, and
@@ -44,7 +45,9 @@ public:
     //! Heat flow rate through the wall (W).
     /*!
      * The heat flux is given by
-     * \f[ Q = h A (T_{left} - T_{right}) + A G(t) \f]
+     * \f[
+     *     Q = h A (T_{left} - T_{right}) + A G(t)
+     * \f]
      * where *h* is the heat transfer coefficient, *A* is the wall area, and
      * *G(t)* is a specified function of time. Positive values denote a flux
      * from left to right.
@@ -126,14 +129,12 @@ public:
         return (m_left != 0 && m_right != 0);
     }
 
-    //! Return a reference to the Reactor or Reservoir to the left
+    //! Return a reference to the Reactor or Reservoir to the left of the wall.
-    //! of the wall.
     ReactorBase& left() const {
         return *m_left;
     }
 
-    //! Return a reference to the Reactor or Reservoir to the
+    //! Return a reference to the Reactor or Reservoir to the right of the wall.
-    //! right of the wall.
     const ReactorBase& right() {
         return *m_right;
     }
@@ -171,8 +172,8 @@ public:
     //! Write the coverages of the left or right surface into array `cov`.
     void getCoverages(int leftright, doublereal* cov);
 
-    //! Set the coverages in the surface phase object to the
+    //! Set the coverages in the surface phase object to the values for this
-    //! values for this wall surface.
+    //! wall surface.
     void syncCoverages(int leftright);
 
     //! Number of sensitivity parameters associated with reactions on the left

include/cantera/zeroD/flowControllers.h

@@ -1,8 +1,4 @@
-/**
+//! @file flowControllers.h Some flow devices derived from class FlowDevice.
- *  @file flowControllers.h
- *
- *  Some flow devices derived from class FlowDevice.
- */
 
 // Copyright 2001  California Institute of Technology
 

src/zeroD/ConstPressureReactor.cpp

@@ -1,7 +1,4 @@
-/**
+//! @file ConstPressureReactor.cpp A constant pressure zero-dimensional reactor
- *  @file ConstPressureReactor.cpp A constant pressure zero-dimensional
- *      reactor
- */
 
 // Copyright 2001  California Institute of Technology
 

src/zeroD/FlowReactor.cpp

@@ -1,6 +1,4 @@
-/**
+//! @file FlowReactor.cpp A steady-state plug flow reactor
-*  @file FlowReactor.cpp A steady-state plug flow reactor
-*/
 
 // Copyright 2001  California Institute of Technology
 
@@ -94,11 +92,10 @@ void FlowReactor::evalEqs(doublereal time, doublereal* y,
     // distance equation
     ydot[0] = m_speed;
 
-    // speed equation. Set m_fctr to a large value, so that rho*u is
+    // speed equation. Set m_fctr to a large value, so that rho*u is held fixed
-    // held fixed
     ydot[1] = m_fctr*(m_speed0 - m_thermo->density()*m_speed/m_rho0);
 
-    /* species equations */
+    // species equations //
     const vector_fp& mw = m_thermo->molecularWeights();
 
     if (m_chem) {

src/zeroD/IdealGasConstPressureReactor.cpp

@@ -1,7 +1,4 @@
-/**
+//! @file ConstPressureReactor.cpp A constant pressure zero-dimensional reactor
- *  @file ConstPressureReactor.cpp A constant pressure zero-dimensional
- *      reactor
- */
 
 // Copyright 2001  California Institute of Technology
 

src/zeroD/IdealGasReactor.cpp

@@ -1,6 +1,4 @@
-/**
+//! @file IdealGasReactor.cpp A zero-dimensional reactor
- *  @file IdealGasReactor.cpp A zero-dimensional reactor
- */
 
 #include "cantera/zeroD/IdealGasReactor.h"
 #include "cantera/zeroD/FlowDevice.h"

src/zeroD/Reactor.cpp

@@ -1,6 +1,4 @@
-/**
+//! @file Reactor.cpp A zero-dimensional reactor
- *  @file Reactor.cpp A zero-dimensional reactor
- */
 
 // Copyright 2001  California Institute of Technology
 
@@ -229,13 +227,10 @@ void Reactor::evalEqs(doublereal time, doublereal* y,
         dYdt[k] -= Y[k] * mdot_surf / m_mass;
     }
 
-    /*
+    // Energy equation.
-     *  Energy equation.
+    // \f[
-     *  \f[
+    //     \dot U = -P\dot V + A \dot q + \dot m_{in} h_{in} - \dot m_{out} h.
-     *  \dot U = -P\dot V + A \dot q + \dot m_{in} h_{in}
+    // \f]
-     * - \dot m_{out} h.
-     * \f]
-     */
     if (m_energy) {
         ydot[2] = - m_thermo->pressure() * m_vdot - m_Q;
     } else {

src/zeroD/ReactorBase.cpp

@@ -1,6 +1,4 @@
-/**
+//! @file ReactorBase.cpp
- *  @file ReactorBase.cpp
- */
 
 // Copyright 2001  California Institute of Technology
 

src/zeroD/ReactorFactory.cpp

@@ -1,6 +1,5 @@
-/**
+//! @file ReactorFactory.cpp
- *  @file ReactorFactory.cpp
+
- */
 // Copyright 2006  California Institute of Technology
 
 #include "cantera/zeroD/ReactorFactory.h"
@@ -30,9 +29,6 @@ static int _itypes[] = {ReservoirType, ReactorType, ConstPressureReactorType,
                         IdealGasConstPressureReactorType
                        };
 
-/**
- * This method returns a new instance of a subclass of ThermoPhase
- */
 ReactorBase* ReactorFactory::newReactor(const std::string& reactorType)
 {
     int ir=-1;